Apple has released iTunes 11.2.1 tonight, a minor update which indeed fixes this missing /Users folder bug, even though the release notes don’t mention it (thanks Ex!). Update: Apple explains the fix in this support document.
How to install iTunes 11.2.1? The update is available in the Mac App Store (on your Mac) in the Updates tab. If you’re missing your /Users directory, this update should bring it back. Let us know how it works out for you.